@@ 19246,77 19246,77 @@ large-scale data-analysis.")
"1dvh23fx52m59y6304xi2j2pl2hiqadlqg8jyv2pm14j1hy71ych"))))
(build-system perl-build-system)
(arguments
- `(#:modules ((guix build perl-build-system)
+ (list
+ #:modules '((guix build perl-build-system)
(guix build utils)
(srfi srfi-26))
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'hardcode-references
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((bedtools (assoc-ref inputs "bedtools"))
- (r (assoc-ref inputs "r-minimal")))
- (substitute* '("scripts/python/getEigenVectors.py"
- "scripts/python/matrix2EigenVectors.py")
- (("bedtools intersect")
- (string-append bedtools "/bin/bedtools intersect")))
- (substitute* "lib/cworld/dekker.pm"
- (("bedtools --version")
- (string-append bedtools "/bin/bedtools --version")))
- (substitute* '("scripts/perl/correlateMatrices.pl"
- "scripts/perl/matrix2scaling.pl"
- "scripts/perl/matrix2distance.pl"
- "scripts/perl/coverageCorrect.pl"
- "scripts/perl/matrix2anchorPlot.pl"
- "scripts/python/matrix2EigenVectors.py"
- "scripts/python/matrix2insulation-lite.py"
- "scripts/perl/matrix2compartment.pl"
- "scripts/perl/anchorPurge.pl"
- "scripts/perl/applyCorrection.pl"
- "scripts/perl/compareInsulation.pl"
- "scripts/perl/fillMissingData.pl"
- "scripts/perl/matrix2loess.pl"
- "scripts/python/getEigenVectors.py"
- "scripts/perl/aggregateBED.pl"
- "scripts/perl/collapseMatrix.pl"
- "scripts/perl/matrix2direction.pl"
- "scripts/perl/singletonRemoval.pl"
- "lib/cworld/dekker.pm"
- "scripts/perl/matrix2insulation.pl")
- (("(`|\")Rscript" _ pre)
- (string-append pre r "/bin/Rscript"))))))
- (add-after 'install 'install-scripts
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (share (string-append out "/share/cworld-dekker")))
- (mkdir-p share)
- (copy-recursively "scripts" share)
-
- ;; Make all scripts executable and wrap them.
- (let ((r (find-files share "\\.R$"))
- (py (find-files share "\\.py$"))
- (pl (find-files share "\\.pl$"))
- (wrap (lambda* (script var #:optional (extra ""))
- (let ((path (string-append (getenv var)
- extra)))
- (wrap-program script
- `(,var ":" prefix (,path)))))))
- (for-each (cut chmod <> #o555) (append r py pl))
- (for-each (cut wrap <> "PERL5LIB"
- (string-append ":" out
- "/lib/perl5/site_perl"))
- pl)
- (for-each (cut wrap <> "GUIX_PYTHONPATH") py))))))))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'hardcode-references
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((bedtools #$(this-package-input "bedtools"))
+ (r #$(this-package-input "r-minimal")))
+ (substitute* '("scripts/python/getEigenVectors.py"
+ "scripts/python/matrix2EigenVectors.py")
+ (("bedtools intersect")
+ (string-append bedtools "/bin/bedtools intersect")))
+ (substitute* "lib/cworld/dekker.pm"
+ (("bedtools --version")
+ (string-append bedtools "/bin/bedtools --version")))
+ (substitute* '("scripts/perl/correlateMatrices.pl"
+ "scripts/perl/matrix2scaling.pl"
+ "scripts/perl/matrix2distance.pl"
+ "scripts/perl/coverageCorrect.pl"
+ "scripts/perl/matrix2anchorPlot.pl"
+ "scripts/python/matrix2EigenVectors.py"
+ "scripts/python/matrix2insulation-lite.py"
+ "scripts/perl/matrix2compartment.pl"
+ "scripts/perl/anchorPurge.pl"
+ "scripts/perl/applyCorrection.pl"
+ "scripts/perl/compareInsulation.pl"
+ "scripts/perl/fillMissingData.pl"
+ "scripts/perl/matrix2loess.pl"
+ "scripts/python/getEigenVectors.py"
+ "scripts/perl/aggregateBED.pl"
+ "scripts/perl/collapseMatrix.pl"
+ "scripts/perl/matrix2direction.pl"
+ "scripts/perl/singletonRemoval.pl"
+ "lib/cworld/dekker.pm"
+ "scripts/perl/matrix2insulation.pl")
+ (("(`|\")Rscript" _ pre)
+ (string-append pre r "/bin/Rscript"))))))
+ (add-after 'install 'install-scripts
+ (lambda _
+ (let ((share (string-append #$output "/share/cworld-dekker")))
+ (mkdir-p share)
+ (copy-recursively "scripts" share)
+
+ ;; Make all scripts executable and wrap them.
+ (let ((r (find-files share "\\.R$"))
+ (py (find-files share "\\.py$"))
+ (pl (find-files share "\\.pl$"))
+ (wrap (lambda* (script var #:optional (extra ""))
+ (let ((path (string-append (getenv var)
+ extra)))
+ (wrap-program script
+ `(,var ":" prefix (,path)))))))
+ (for-each (cut chmod <> #o555) (append r py pl))
+ (for-each (cut wrap <> "PERL5LIB"
+ (string-append ":" #$output
+ "/lib/perl5/site_perl"))
+ pl)
+ (for-each (cut wrap <> "GUIX_PYTHONPATH") py))))))))
(inputs
- `(("libgd" ,gd)
- ("perl-gd" ,perl-gd)
- ("bedtools" ,bedtools)
- ("python" ,python-wrapper)
- ("python-scipy" ,python-scipy)
- ("python-numpy" ,python-numpy)
- ("python-matplotlib" ,python-matplotlib)
- ("python-h5py" ,python-h5py)
- ("python-scikit-learn" ,python-scikit-learn)
- ("r-minimal" ,r-minimal)))
+ (list gd
+ perl-gd
+ bedtools
+ python-wrapper
+ python-scipy
+ python-numpy
+ python-matplotlib
+ python-h5py
+ python-scikit-learn
+ r-minimal))
(native-inputs
(list perl-module-build))
(home-page "https://github.com/dekkerlab/cworld-dekker")